This blog is meant to allow Fragment-based Drug Design Practitioners to get together and discuss NON-CONFIDENTIAL issues regarding fragments.

27 October 2014

Fragments vs Bcl-XL – selectively

One of the more popular applications of
fragment-based lead discovery has been targeting protein-protein interactions.
Among these, the BCL-2 family of anti-apoptotic proteins has proven
particularly successful, as exemplified by several compounds in clinical trials
against various cancers. SAR by NMR was used in the discovery of the chemical series that ultimately led to navitoclax, which inhibits both BCL-XL
and BCL-2, and subsequent medicinal chemistry led to a selective inhibitor of
BCL-2, which is now in phase 3 trials. In a recent paper in ACS Med. Chem. Lett., Zhi-Fu Tao and
dozens of collaborators at AbbVie, Genentech, The Walter and Eliza Hall
Institute of Medical Research (WEHI), and the University of Melbourne describe
how fragments contributed to a specific inhibitor of BCL-XL.

High-throughput screening and medicinal
chemistry at WEHI initially led to compound 1, a selective inhibitor of BCL-XL,
which was optimized to the potent WEHI-539 in collaboration with Genentech.
This molecule had some pharmacokinetic liabilities, so, in collaboration with AbbVie,
the researchers came up with compound 4. To optimize this molecule further,
they turned to SAR by NMR, which entails screening fragments in the presence of
an initial binder to find fragments that bind to a second site.

The researchers used 2-dimensional NMR (1H–13C-HSQC)
to screen a complex of BCL-XL and compound 1against 875 highly
soluble fragments in pools of five, with each fragment present at 5 mM!
Compound 6 was one of the better binders, and NMR-guided docking revealed that
it bound close to compound 1, suggesting a fragment linking approach. This
proved successful, though as with many linking studies it was
critical to get the linker just right: shortening or lengthening the linker by
a single methylene decreased affinity by more than two orders of magnitude (middle right).

Although remarkably potent, the best linked compound is
also quite lipophilic (ClogP = 6.2), and adding human plasma to the assay
caused a marked loss in potency, suggesting it gets sopped up by serum
albumin. Previous work on navitoclax had shown that introducing a basic amino
group could decrease binding to albumin, and doing this while simplifying the
fragment ultimately led to A-1155463, which showed extraordinary biochemical
and cell-based potency as well as on-target activity in mice.

This seems to be a classic case of
fragment-assisted drug discovery, where fragments played a supporting role in a
larger medicinal chemistry program rather than taking center stage. In this
case one could argue that the role was relatively minor, and that it may have
been possible to use conventional approaches to get from WEHI-539 to A-1155463.
Nonetheless, the information provided by the fragments likely led to a fuller
understanding of the binding pocket, and in difficult targets like this it is
important to use all the tools at one’s disposal.